From patchwork Wed Jul 24 18:22:03 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 14768 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 2416A17270; Wed, 24 Jul 2019 19:23:18 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,FREEMAIL_FROM, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id D4F2A1726E for ; Wed, 24 Jul 2019 19:23:17 +0100 (BST) Received: from localhost ([::1]:54034 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLv3-00046O-IL for patchwork@mira.cbaines.net; Wed, 24 Jul 2019 14:23:17 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41510) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLux-0003kA-Bg for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:12 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuw-00006D-1K for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:11 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:57433) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuv-00005z-SU for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:09 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1hqLuv-0005QO-NU for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:09 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#36799] [PATCH 10/11] gnu: Add r-mixomics. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 24 Jul 2019 18:23:09 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 36799 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 36799@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.156399257020664 (code B ref -1); Wed, 24 Jul 2019 18:23:09 +0000 Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:50 +0000 Received: from localhost ([127.0.0.1]:37999 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLub-0005NC-Os for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:50 -0400 Received: from lists.gnu.org ([209.51.188.17]:53309) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuI-0005Li-U9 for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:31 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41156) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuH-0003JD-NB for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:30 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuG-0007LN-E5 for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:29 -0400 Received: from mail-wr1-x444.google.com ([2a00:1450:4864:20::444]:37543) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuG-0007KG-7w for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:28 -0400 Received: by mail-wr1-x444.google.com with SMTP id n9so22935346wrr.4 for ; Wed, 24 Jul 2019 11:22:28 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=OSVrzdIYMqZK1JmBVmn3id+dsxL+4LAG2m5E4h3cW3M=; b=sha95n4lGaGvY2bGThdgOf385qekX03bv61eBfpv2LEvAVZRVjU63K52ANguH9HtTz 04XNqFy8KXEQX+hDGGtS8ua4fn6ISFhGcSag6a0gUB1k2Lb3BM7oIFshmokDRh7cjiIO 6MVRaWwz/kNYDrDhuABoFnTHbei4fzV8ZRGfEXCsy+QHfmj9xzRfoJ5VzzRn3KZD9BHW Qbci9qgUSjY72Gqp2GxX73Rn+oqAS4bRrwNdUf1jxORL4nqh+2gW8JKKeIvr1JrCjkQX 2yaxMYuWcMc0uTHWVAw97UEKDg5ZxaPGwdIORcK3eU9jrW8UVjh4A3//Vu+i0ywKufQ1 lKpQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=OSVrzdIYMqZK1JmBVmn3id+dsxL+4LAG2m5E4h3cW3M=; b=NYjBxCF1GICvMFMKa1ZbaSVZqFtFj9hfBXAX5CfTPUYf7cAFMmLkVfwxkYXnM7Xwxq XW7bwhuxaaN7IRgMlutbKFRRLlLhIc9kL0GN2r60hz+SlmbIkzyu705NRl56TCb7Pyct xHzi3MvRoG8j/yQXxM5zUCIqq0hs8SPVh6RkdEPbySU8f75OCh8pa9u99Q/2s50Rc3p3 J3pJhPpoIELMqb0fIHontAAjwMnPzc9horqZeHZrWAI4MtK9Vi16jeo/qAo9Q077B29j QessCVsxH8KbsCUmTjUuzVmrsSzYLbZtFk+vARDF0er86HhogxVgLHz5tI31VYufYvpM U/Fg== X-Gm-Message-State: APjAAAWSKC6b8Y5X4Sv3PJV8B8coepefU4Jc9S0QOePuT8oK244TXUSO hle41XYFNndUCmqG9ZUnDCVfa641 X-Google-Smtp-Source: APXvYqzyl11IBqOyaqgmhhrD+fF562RdIWpPtMnE28DsPNfTMy9rUwVULK1zqzOsXyGJRCib3fIPHg== X-Received: by 2002:adf:ec0f:: with SMTP id x15mr54221988wrn.165.1563992546975; Wed, 24 Jul 2019 11:22:26 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.26 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:26 -0700 (PDT) From: zimoun Date: Wed, 24 Jul 2019 20:22:03 +0200 Message-Id: <20190724182204.6818-11-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.22.0 In-Reply-To: <20190724182204.6818-1-zimon.toutoune@gmail.com> References: <20190724182204.6818-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-mixomics): New variable. --- gnu/packages/bioconductor.scm | 54 +++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dd6570ed17..64625aedd4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4959,3 +4959,57 @@ and to both short and long sequence reads.") "FlowSOM offers visualization options for cytometry data, by using Self-Organizing Map clustering and Minimal Spanning Trees.") (license license:gpl2+))) +(define-public r-mixomics + (package + (name "r-mixomics") + (version "6.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "mixOmics" version)) + (sha256 + (base32 + "1f08jx35amn3sfcmqb96mjxxsm6dnpzhff625z758x1992wj4zsk")))) + (properties `((upstream-name . "mixOmics"))) + (build-system r-build-system) + (propagated-inputs + `(("r-corpcor" ,r-corpcor) + ("r-dplyr" ,r-dplyr) + ("r-ellipse" ,r-ellipse) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-igraph" ,r-igraph) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-matrixstats" ,r-matrixstats) + ("r-rarpack" ,r-rarpack) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-reshape2" ,r-reshape2) + ("r-tidyr" ,r-tidyr))) + (home-page "http://www.mixOmics.org") + (synopsis "Omics Data Integration Project") + (description + "Multivariate methods are well suited to large omics data sets where the +number of variables (e.g. genes, proteins, metabolites) is much larger than +the number of samples (patients, cells, mice). They have the appealing +properties of reducing the dimension of the data by using instrumental +variables (components), which are defined as combinations of all variables. +Those components are then used to produce useful graphical outputs that enable +better understanding of the relationships and correlation structures between +the different data sets that are integrated. mixOmics offers a wide range of +multivariate methods for the exploration and integration of biological +datasets with a particular focus on variable selection. The package proposes +several sparse multivariate models we have developed to identify the key +variables that are highly correlated, and/or explain the biological outcome of +interest. The data that can be analysed with mixOmics may come from high +throughput sequencing technologies, such as omics data (transcriptomics, +metabolomics, proteomics, metagenomics etc) but also beyond the realm of +omics (e.g. spectral imaging). The methods implemented in mixOmics can also +handle missing values without having to delete entire rows with missing data. +A non exhaustive list of methods include variants of generalised Canonical +Correlation Analysis, sparse Partial Least Squares and sparse Discriminant +Analysis. Recently we implemented integrative methods to combine multiple +data sets: N-integration with variants of Generalised Canonical Correlation +Analysis and P-integration with variants of multi-group Partial Least +Squares.") + (license license:gpl2+)))